The unprecedented complexity of the transcriptomic data obtained in recent years creates opportunities for new genomic studies aimed at interpolating regulatory code of gene expression and tracing genome evolution. We report here the identification and characterization of a set of 851 intergenic loci that represent transcribed gene fragments (TGFs) ectopically duplicated from 1030 non-transposable element (non-TE) donor genes in the rice genome. We analyzed the genomic context of the TGFs and donor genes. We show that the TGFs have adopted transcriptional orientation and pattern independent of the donor genes. We further show that TGFs have undergone relaxed purifying selection, consistent with their being pseudogenized. We found that the donor genes, which are biased toward certain molecular functions, exhibit an accelerated evolution rate comparing to the genome average. Our results demonstrated a large number of actively TGFs in the rice genome and shed light on the origin, mode of action and function of the TGFs.

Abstract Summary: NMPP package is a bundle of user-customized tools based on established algorithms and methods to process self-designed NimbleGen microarray data. It features a command-line-based integrative processing procedure that comprises five major functional components, namely the raw microarray data parsing and integrating module, the array spatial effect smoothing and visualization module, the probe-level multi-array normalization module, the gene expression intensity summarization module and the gene expression status inference module. Availability: Contact: [email protected] Supplementary information: The supplementary materials, figures, testing dataset, software instructions and a typical workflow of using NMPP package are accessible through the above homepage.